The secondary index CF's are marked as no longer required / marked as compacted. under 1.x they would then be deleted reasonably quickly, and definitely deleted after a restart.

Is there a zero length .Compacted file there ?

Also, when adding a new node to the ring the new node will build indexes for the ones that supposedly donít exist any longer. Is this supposed to happen? Would this have happened if I had deleted the old SSTables from the previously existing nodes?

Check you have a consistent schema using describe cluster in the CLI. And check the schema is what you think it is using show schema.

Another trick is to do a snapshot. Only the files in use are included the snapshot.

I have a few column families that I decided to get rid of the secondary indexes on. I see that there arenít any new index SSTables being created, but all of the old ones remain (some from as far back as September). Is it safe to just delete then when the node is offline? Should I run clean-up or scrub?

Also, when adding a new node to the ring the new node will build indexes for the ones that supposedly donít exist any longer. Is this supposed to happen? Would this have happened if I had deleted the old SSTables from the previously existing nodes?

The nodes in question have either been upgraded from v0.8.1 => v1.0.2 (scrubbed at this time) => v1.0.6 or from v1.0.2 => v1.0.6. The secondary index was dropped when the nodes were version 1.0.6. The new node added was also 1.0.6.